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Author Topic:   Discussion of Phylogenetic Methods
Dr Adequate
Member
Posts: 15472
Joined: 07-20-2006
Member Rating: 3.9


Message 256 of 288 (796291)
12-28-2016 10:55 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
d.p.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has not yet responded

  
Taq
Member
Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


Message 257 of 288 (796292)
12-28-2016 11:02 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:

Pointing to the strength of current phylogenies is irrelevant.

Evolution did not predict those phylogenies.

Yes, it did.

"It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life."
Emile Zuckerkandl and Linus Pauling, discussing the possibility of the twin nested hierarchy before the first molecular phylogenies had been made. (1965) "Evolutionary Divergence and Convergence in Proteins." in Evolving Genes and Proteins, p. 101.

Evolution could have occurred an infinite number of ways, producing a near infinite number of potential phylogenies.

But they would all have a phylogenetic signal. That is the prediction. Yes, evolution could have played out differently. However, whatever species did evolve they would produce a phylogeny.

For any one of these supposed "trends" you show me I could a fossil sequence that is out of order. One of the more interesting examples is advanced tetrapod footprints appearing in rocks roughly 20 million years older than the 'fishapods' that were supposed to just be starting to develop proto-limbs to walk on.

That is not out of order since those tracks appear after lobe finned fish appear.

You seem to be under the mistaken idea that Tiktaalik is a direct ancestor. Tiktaalik could have been a sister taxa that preserved some of the transitional features found in the direct lineage. Even Darwin addressed this:

"In looking for the gradations by which an organ in any species has been perfected, we ought to look exclusively to its lineal ancestors; but this is scarcely ever possible, and we are forced in each case to look to species of the same group, that is to the collateral descendants from the same original parent-form, in order to see what gradations are possible, and for the chance of some gradations having been transmitted from the earlier stages of descent, in an unaltered or little altered condition."--Charles Darwin, "Origin of Species"
http://www.talkorigins.org/faqs/origin/chapter6.html

Your view of evolution is completely wrong. According to your misguided view, there should be just one species in the whole of Earth, the direct ancestor of a single lineage. Guess what? Lineages branch off and go in different directions. Some of those branched off lineages, what Darwin calls collateral descendants and what modern biologists call sister taxa, keep some of the ancestral features that are lost in the other taxa that have branched off. This makes them transitional species because they have preserved the mix of features that would have been found in the transition in the other lineages.


This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has responded

Replies to this message:
 Message 260 by vaporwave, posted 12-29-2016 8:07 AM Taq has responded

  
vaporwave
Member
Posts: 66
Joined: 12-17-2016


Message 258 of 288 (796359)
12-29-2016 7:39 AM
Reply to: Message 251 by RAZD
12-28-2016 10:07 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Please note that this is ~18 million years older than previous tetrapod finds, not the transitional "fishapods" -- that difference is ~10 million years.

Curiously, that is not so much "out of order" as it is that the "order" (sequence) is not fully determined, because evidence is lacking.

So when fossil "transitions" lie in geologic order, then it is evidence for evolution and when the inferred transition is out of geological order then it is simply "not fully determined because evidence is lacking" ... seems convenient.

Actually this wouldn't really bother me except evolutionists are constantly showing off cherry-picked examples of the former while concealing the latter, (providing they are not ignorant of it themselves.)

However, reality cares not a whit for how evolution could occur, and that is irrelevant to what did occur.

But the evolutionists in this discussion seem quite concerned about what 'could' occur, since your arguments continually circle back to how a designer 'could' create life, and why you claim this weakens the argument from design.

All I'm doing is applying the same standard to common ancestry.

If the traits of animals had evolved to be different than what we see today, then we'd simply have a different story of common descent.
... And it would still show the patterns of evolution and nested hierarchies

But nested hierarchies themselves are not evidence for evolution. They may be a requirement of evolution, but that doesn't mean they explicitly point to evolution.

And if common ancestry could potentially explain trillions of different nested hierarchies, then how strong of a theory is it really that it can explain one of them?


This message is a reply to:
 Message 251 by RAZD, posted 12-28-2016 10:07 AM RAZD has responded

Replies to this message:
 Message 259 by JonF, posted 12-29-2016 8:00 AM vaporwave has responded
 Message 261 by Taq, posted 12-29-2016 10:43 AM vaporwave has responded
 Message 263 by RAZD, posted 12-29-2016 10:47 AM vaporwave has not yet responded
 Message 264 by Dr Adequate, posted 12-29-2016 11:36 AM vaporwave has not yet responded
 Message 265 by Tangle, posted 12-29-2016 11:53 AM vaporwave has not yet responded

    
JonF
Member
Posts: 3483
Joined: 06-23-2003
Member Rating: 2.8


Message 259 of 288 (796362)
12-29-2016 8:00 AM
Reply to: Message 258 by vaporwave
12-29-2016 7:39 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
And if common ancestry could potentially explain trillions of different nested hierarchies, then how strong of a theory is it really that it can explain one of them?

Very strong. There are octillions to the octillionth power of possible patterns. The number of possible nested hierarchies is an infinitesimal fraction of the total. Nested hierarchies do not arise by chance. They are the result of a process.

Common ancestry explains why such a pattern \[b\]must\[b\] arise.

Got any other explanation that \[b\]must\[b\] produce a nested hierarchy? GOrt any other explanation that can be reasonably expected to produce a nested hierarchy?


This message is a reply to:
 Message 258 by vaporwave, posted 12-29-2016 7:39 AM vaporwave has responded

Replies to this message:
 Message 267 by vaporwave, posted 12-30-2016 7:08 AM JonF has responded

  
vaporwave
Member
Posts: 66
Joined: 12-17-2016


Message 260 of 288 (796363)
12-29-2016 8:07 AM
Reply to: Message 257 by Taq
12-28-2016 11:02 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Yes, it did.

"It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life."
Emile Zuckerkandl and Linus Pauling, discussing the possibility of the twin nested hierarchy before the first molecular phylogenies had been made. (1965) "Evolutionary Divergence and Convergence in Proteins." in Evolving Genes and Proteins, p. 101.

This is a prediction that the already observed pattern of life will be maintained with increased data. (e.g. mammals will continue to find highest trait similarity among mammals, etc.)

You can't say evolution predicted the general classification of animal groups since this was already achieved to a great degree before the theory was even off the ground. (And evolution couldn't predict this even in principle)

Evolution came along and constructed a narrative around that pattern of life. (as it could have a multitude of different patterns)

But they would all have a phylogenetic signal.

So what, a series of computer software has a "phylogenetic signal".

To rule out evolution, there would have to be a significant enough violation of the signal to be irreconcilable to any potential common ancestry narrative, something that couldn't be dismissed as a lack of data.


This message is a reply to:
 Message 257 by Taq, posted 12-28-2016 11:02 AM Taq has responded

Replies to this message:
 Message 262 by Taq, posted 12-29-2016 10:45 AM vaporwave has not yet responded

    
Taq
Member
Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


Message 261 of 288 (796368)
12-29-2016 10:43 AM
Reply to: Message 258 by vaporwave
12-29-2016 7:39 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:

So when fossil "transitions" lie in geologic order, then it is evidence for evolution and when the inferred transition is out of geological order then it is simply "not fully determined because evidence is lacking" ... seems convenient.

Your example is not out of order. Tiktaalik shows up well after the first lobe finned fish. You might as well claim that the platypus is out of order because it has outlived some placental mammal species. You might as well claim that a fish fossil is out of order if it is 10 million years old because mammals show up in the fossil record more than 60 million years ago. Do you see your flaw or not?

But the evolutionists in this discussion seem quite concerned about what 'could' occur, since your arguments continually circle back to how a designer 'could' create life, and why you claim this weakens the argument from design.

Dr Adequate explained it perfectly in post 255

quote:
And if biology was not constrained by evolution, there would be a still greater number of non-phylogenies.

Your argument is like saying that the theory of gravity isn't supported by observing the dynamics of the solar system, because we can imagine an infinite number of alternate solar systems with different planets at different distances from the sun which also obeyed the theory of gravity.

Well, this is true, the theory of gravity doesn't predict the number of the planets, or their distance from the sun, or their sizes. But it does predict, for example, that they will obey Kepler's laws --- and we can imagine many more solar systems that don't.

We put a theory to the test by testing the things it does predict; it is irrelevant to note that there are features of the solar system that it doesn't predict, that could be changed and still be compatible with the theory.


Is the theory of gravity falsified because another solar system has planets with different orbits than the ones found in this solar system? No.

The prediction for evolution is that whatever species do evolve they will fall into a nested hierarchy just as planets, no matter their composition or distance from their star, will follow the laws of gravity.

A designer has no such restrictions. A designer can design species so that they violate a nested hierarchy. We see that with human designs where paintings, buildings, computer programs, and automobiles do not form a nested hierarchy.

But nested hierarchies themselves are not evidence for evolution.

Yes, they are. When the pattern of shared derived features matches what evolution will produce then it is evidence for evolution.

And if common ancestry could potentially explain trillions of different nested hierarchies, then how strong of a theory is it really that it can explain one of them?

The same way that the theory of gravity can explain the orbits of trillions of different solar systems.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 258 by vaporwave, posted 12-29-2016 7:39 AM vaporwave has responded

Replies to this message:
 Message 268 by vaporwave, posted 12-30-2016 7:18 AM Taq has responded
 Message 271 by vaporwave, posted 12-30-2016 8:57 AM Taq has responded

  
Taq
Member
Posts: 6014
Joined: 03-06-2009
Member Rating: 3.6


(1)
Message 262 of 288 (796369)
12-29-2016 10:45 AM
Reply to: Message 260 by vaporwave
12-29-2016 8:07 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:

This is a prediction that the already observed pattern of life will be maintained with increased data. (e.g. mammals will continue to find highest trait similarity among mammals, etc.)

That is false. In 1965 they had barely discovered DNA. They had no real data demonstrating that DNA phylogenies would match phylogenies based on morphology.

So what, a series of computer software has a "phylogenetic signal".

Prove it. Until you do, the evidence is in support of evolution.

To rule out evolution, there would have to be a significant enough violation of the signal to be irreconcilable to any potential common ancestry narrative, something that couldn't be dismissed as a lack of data.

Precisely. Such violations would be child's play for a designer. In fact, humans do it all of the time.


This message is a reply to:
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RAZD
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Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


(1)
Message 263 of 288 (796371)
12-29-2016 10:47 AM
Reply to: Message 258 by vaporwave
12-29-2016 7:39 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
So when fossil "transitions" lie in geologic order, then it is evidence for evolution and when the inferred transition is out of geological order then it is simply "not fully determined because evidence is lacking" ... seems convenient.

In this case we have two pieces of evidence -- the footprints and tiktaalik. That is hardly a plethora of evidence.

We also have evidence of transitional species existing long after their developed offspring began existing, so an overlap is not out of the ordinary. I could point to coelacanth existing today, 65 million years after first appearing in the fossil record. Does that make today's specimens out of order? Yes they are different species (coelacanth is a family level clade), but we also don't know if the same is true of tiktaalik.

Actually this wouldn't really bother me except evolutionists are constantly showing off cherry-picked examples of the former while concealing the latter, (providing they are not ignorant of it themselves.)

Or they are just presenting the evidence that is easiest to understand. Perhaps you could give us an example of evidence being concealed? Obviously tiktaalik and the footprints are not concealed.

But the evolutionists in this discussion seem quite concerned about what 'could' occur, since your arguments continually circle back to how a designer 'could' create life, and why you claim this weakens the argument from design.

No. That is not to say evolutionists are concerned at all about what 'could' occur, just that they are putting it in contrast to other concepts.

We could as easily talk about Lamarkism to evaluate what could occur vs what does occur. Lamarkism would not necessarily produce nested hierarchies.

All I'm doing is applying the same standard to common ancestry.

No, you are cherry picking a small number of unresolved cases and claiming that it throws the whole concept of common ancestry out the window. It doesn't.

But nested hierarchies themselves are not evidence for evolution. They may be a requirement of evolution, but that doesn't mean they explicitly point to evolution.

They are what we expect\predict from evolution; we see evidence in life today, in the DNA and in the fossil record of it happening. That is a test that validates the expectation\prediction.

We do NOT see non-nested hierarchies, such as feathers on bats or whales with gills, ... except in very limited cases of horizontal gene transfer between bacteria.

And if common ancestry could potentially explain trillions of different nested hierarchies, then how strong of a theory is it really that it can explain one of them?

I think you meant "can't explain one of them?"

As I said above:

No, you are cherry picking a small number of unresolved cases and claiming that it throws the whole concept of common ancestry out the window. It doesn't.

Still very strong, as in high confidence that it will continue to apply to those trillions of situations, because the inability to explain a certain small number of situations where not all the facts are known is quite different from having something that actually invalidates the concept of common ancestry. Any system that models evidence with >99.99% accuracy is considered very accurate.

In science we expect to see anomalies rather than wholesale compliance, because that's the way reality works. Usually they are sought out to see if some new idea can be developed (a new way to detect phylogenies in rapidly evolving species, more evidence around the dates of the footprints and tiktallik, etc) as this is where names are made.

It is said that the verbal sign of a new discovery is not "eureka" but "that's curious ... "

Enjoy

Edited by RAZD, : .

Edited by RAZD, : .


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This message is a reply to:
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Dr Adequate
Member
Posts: 15472
Joined: 07-20-2006
Member Rating: 3.9


(1)
Message 264 of 288 (796378)
12-29-2016 11:36 AM
Reply to: Message 258 by vaporwave
12-29-2016 7:39 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Actually this wouldn't really bother me except evolutionists are constantly showing off cherry-picked examples of the former while concealing the latter ...

How do you know what they're concealing? Are you dressing up in evolutionist robes and infiltrating their secret conclaves? Or are they in fact not concealing it?

But nested hierarchies themselves are not evidence for evolution. They may be a requirement of evolution, but that doesn't mean they explicitly point to evolution.

Once more you are raising an objection which if taken seriously would destroy the whole of science and the scientific method.


This message is a reply to:
 Message 258 by vaporwave, posted 12-29-2016 7:39 AM vaporwave has not yet responded

  
Tangle
Member
Posts: 4405
From: UK
Joined: 10-07-2011
Member Rating: 2.9


(1)
Message 265 of 288 (796380)
12-29-2016 11:53 AM
Reply to: Message 258 by vaporwave
12-29-2016 7:39 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporware writes:

But nested hierarchies themselves are not evidence for evolution. They may be a requirement of evolution, but that doesn't mean they explicitly point to evolution.

This is perverse.

If nested hierarchies are a requirement for evolution, and we find that without exception nested heirarchies exist in all biological systems, then I'd say that's smoking gun evidence.

Had we not found hierarchies we wouldn't find evolution. You are attempting to find a tautology - but you can't can you? The two must co-exist for either to be true. ToE requires descent, descent requires nested hierarchies. The ToE is just a way of describing what happens and has happened in nature. (And remarkably, how.)

Any evidence of your own yet? Want to explain how creationism works?


Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien.

"Life, don't talk to me about life" - Marvin the Paranoid Android

"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.


This message is a reply to:
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jar
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Posts: 28432
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.6


Message 266 of 288 (796384)
12-29-2016 12:16 PM
Reply to: Message 265 by Tangle
12-29-2016 11:53 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
You just don't understand. You think holes in the target are evidence the arrow hit the target but the arrow may have hit the target but never made a hole or holes may have been made even though the target was missed or the holes may have been made by target eating worms or the target may have been designed with holes in it or ...

My Sister's Website: Rose Hill Studios My Website: My Website

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vaporwave
Member
Posts: 66
Joined: 12-17-2016


Message 267 of 288 (796442)
12-30-2016 7:08 AM
Reply to: Message 259 by JonF
12-29-2016 8:00 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
There are octillions to the octillionth power of possible patterns. The number of possible nested hierarchies is an infinitesimal fraction of the total. Nested hierarchies do not arise by chance. They are the result of a process.

Another invocation of the hypothetical 'random-creature-generator' - (If not evolution, then we should expect the pattern of life to look like spaghetti thrown against the wall)

If that's the bizarre comparison you need to draw to make common ancestry seem more likely, then have at it.


This message is a reply to:
 Message 259 by JonF, posted 12-29-2016 8:00 AM JonF has responded

Replies to this message:
 Message 269 by JonF, posted 12-30-2016 8:12 AM vaporwave has responded
 Message 273 by Dr Adequate, posted 12-30-2016 10:20 AM vaporwave has not yet responded
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vaporwave
Member
Posts: 66
Joined: 12-17-2016


Message 268 of 288 (796443)
12-30-2016 7:18 AM
Reply to: Message 261 by Taq
12-29-2016 10:43 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Your example is not out of order. Tiktaalik shows up well after the first lobe finned fish

So footprints showing up 10-20 million years before the limbs that would make them is not out of order. You have a strange definition of order.

You might as well claim that a fish fossil is out of order if it is 10 million years old because mammals show up in the fossil record more than 60 million years ago. Do you see your flaw or not?

Obviously ancestors can live contemporaneously or outlast their descendants. I'm not arguing this is some kind of disproof of evolution.

It's funny you guys make such a big deal out of these supposed chronological fossil transitions and then when a counter-example is pointed out you start hand-waving that the specific order actually doesn't matter. So why were you arguing it in the first place? Just trying to make a sale?


This message is a reply to:
 Message 261 by Taq, posted 12-29-2016 10:43 AM Taq has responded

Replies to this message:
 Message 270 by JonF, posted 12-30-2016 8:31 AM vaporwave has not yet responded
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JonF
Member
Posts: 3483
Joined: 06-23-2003
Member Rating: 2.8


Message 269 of 288 (796445)
12-30-2016 8:12 AM
Reply to: Message 267 by vaporwave
12-30-2016 7:08 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
There are octillions to the octillionth power of possible patterns. The number of possible nested hierarchies is an infinitesimal fraction of the total. Nested hierarchies do not arise by chance. They are the result of a process.

Another invocation of the hypothetical 'random-creature-generator' - (If not evolution, then we should expect the pattern of life to look like spaghetti thrown against the wall)

If that's the bizarre comparison you need to draw to make common ancestry seem more likely, then have at it.


I notice you failed to address the point; common ancestry requires a nested hierarchy. Nobody has proposed any other process that requires a nested hierarchy. If some other process produced what we see why did it produce a nested hierarchy instead of the almost innumerable other possibilities?
This message is a reply to:
 Message 267 by vaporwave, posted 12-30-2016 7:08 AM vaporwave has responded

Replies to this message:
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JonF
Member
Posts: 3483
Joined: 06-23-2003
Member Rating: 2.8


Message 270 of 288 (796446)
12-30-2016 8:31 AM
Reply to: Message 268 by vaporwave
12-30-2016 7:18 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
So footprints showing up 10-20 million years before the limbs that would make them is not out of order. You have a strange definition of order.

False premise. Footprints similar to Tiktallik's showing up 10-20 million years before the Tiktalliks we've found is not prima facie out of order. Characteristics can easily persist for many millions of years.

E.g. if we found a footprint of an American Alligator 150 million years old, and we see a footprint made by an American Alligator today, they would be the same. Are they out of order?


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